Merge pull request #28 from Sydney-Informatics-Hub/part-2

part 2 typos, small edits
Sydney-Informatics-Hub · Sep 25, 2024 · b22fa97 · b22fa97
2 parents 2b433b8 + 86dcb67
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diff --git a/docs/part2/00_intro.md b/docs/part2/00_intro.md
@@ -116,8 +116,6 @@ Having reviewed the bash scripts, we've decided to keep its modular structure an
 
 ![](./img/2.0_workflow.png)
 
-> Update workflow with folder index output
-
 ## 2.0.5 Nextflowing the workflow
 
 Each lesson in part 2 of our workshop focuses on implementing one process of 

diff --git a/docs/part2/01_salmon_idx.md b/docs/part2/01_salmon_idx.md
@@ -157,8 +157,6 @@ results directory with `mkdir -p "results`.
 More information and other modes can be found on
 [publishDir](https://www.nextflow.io/docs/latest/process.html#publishdir).
 
-You now have a complete process! 
-
 ## 2.1.3 Using containers  
 
 Nextflow recommends using containers to ensure reproducibility and portability
@@ -218,6 +216,8 @@ process INDEX {
 }
 ```
 
+You now have a complete process! 
+
 Usually, containers need to be downloaded using a command such as
 `docker pull [image]`. All containers have been previously downloaded for the
 workshop beforehand.  
@@ -353,7 +353,7 @@ Recall that the specifics of the output are randomly generated (i.e.
 `[chaotic_jones]` and `[de/fef8c4]` in this example).
 
 In this example, the output files for the `INDEX` process is output in
-`work/26/c410b1...`.
+`work/de/fef8c4...`.
 
 You have successfully run your first workflow!  
 
@@ -391,7 +391,7 @@ the process, let’s use the hidden command files saved for this task in the wor
 
     !!! quote "Poll"  
 
-        Why do we no longer see or hardcoded file paths like `results/salmon_index` and `data/ggal/transcriptome.fa` in `.command.sh`?
+        In `.command.sh`, there are no longer hardcoded file paths (e.g. `results/salmon_index` and `data/ggal.transcriptome.fa`). What Nextflow directive and scope enable this?
 
 
 !!! abstract "Summary"

diff --git a/docs/part2/04_multiqc.md b/docs/part2/04_multiqc.md
@@ -195,8 +195,8 @@ Launching `main.nf` [stupefied_minsky] DSL2 - revision: 82245ce02b
 [de/fef8c4] INDEX              | 1 of 1, cached: 1 ✔
 [bb/32a3aa] FASTQC (1)         | 1 of 1, cached: 1 ✔
 [a9/000f36] QUANTIFICATION (1) | 1 of 1, cached: 1 ✔
-/home/setup2/hello-nextflow/part2/work/bb/32a3aaa5e5fd68265f0f34df1c87a5/fastqc_gut_logs
-/home/setup2/hello-nextflow/part2/work/a9/000f3673536d98c8227b393a641871/gut
+/home/user1/part2/work/bb/32a3aaa5e5fd68265f0f34df1c87a5/fastqc_gut_logs
+/home/user1/part2/work/a9/000f3673536d98c8227b393a641871/gut
 ```  
 
 The outputs have been emitted one after the other, meaning that it will be
@@ -258,7 +258,7 @@ Launching `main.nf` [small_austin] DSL2 - revision: 6ab927f137
 [de/fef8c4] INDEX              | 1 of 1, cached: 1 ✔
 [bb/32a3aa] FASTQC (1)         | 1 of 1, cached: 1 ✔
 [a9/000f36] QUANTIFICATION (1) | 1 of 1, cached: 1 ✔
-[/home/setup2/hello-nextflow/part2/work/bb/32a3aaa5e5fd68265f0f34df1c87a5/fastqc_gut_logs, /home/setup2/hello-nextflow/part2/work/a9/000f3673536d98c8227b393a641871/gut]
+[/home/user1/part2/work/bb/32a3aaa5e5fd68265f0f34df1c87a5/fastqc_gut_logs, /home/user1/part2/work/a9/000f3673536d98c8227b393a641871/gut]
 
 ```